First its a means to seed a planet with life, then its a WMD, then it makes zombies, then it makes really rapey aliens.
That was the part I had least trouble with. The first goo is not the same as the other goo, but they're similar. The first goo unzipped the engineer genetically to seed the planet with complex organic molecules. The other goo was a mutagen. Creatures directly affected became zombies (mutants) or penis worms (more mutants), creepy mutant semen should not be used to impregnate Swedish doctors, it creates rapey aliens. Once established via reproduction the rapey aliens became their own thing (in fact, the goo was probably designed to do that given the art on the urn chamber).
Why did the engineers want to erase humanity? Probably a religious thing. One faction decided to play god and another faction disagreed.
I can't explain the actions of the non-robotic characters. Apparently they're just subject to stupidity - not hard to believe considering the writer. The robot made sense, he just thought he was a superior lifeform and decided he could mess with people for fun.